MiRNA-dependent target regulation: Functional characterization of singlenucleotide polymorphisms identified in genome-wide association studies of Alzheimer's disease

Alzheimer's Research and Therapy

Volumn 8, Issue 1, 2016, Pages

  Delay, Charlotte ^a,b,c   Grenier Boley, Benjamin ^a,b,c   Amouyel, Philippe ^a,b,c   Dumont, Julie ^a,b,c   Lambert, Jean Charles ^a,b,c  

^a Univ Lille   (France)

^b INSTITUT PASTEUR DE LILLE   (France)

^c UNIV LILLE   (France)

Author keywords

Alzheimer's disease; FERMT2; MicroRNA; NUP160; PolymiRTS; Single nucleotide polymorphism

Indexed keywords

MICRORNA; MICRORNA 1185 1 3P; MICRORNA 4504; UNCLASSIFIED DRUG; 3' UNTRANSLATED REGION;

3' UNTRANSLATED REGION; ALLELE; ALZHEIMER DISEASE; ARTICLE; BINDING SITE; COMPUTER MODEL; CONTROLLED STUDY; FERMT2 GENE; GENE; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCUS; GENE REPRESSION; GENE TARGETING; GENETIC POLYMORPHISM; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; HUMAN; HUMAN CELL; HUMAN TISSUE; NUP160 GENE; PATHOGENESIS; PRIORITY JOURNAL; REGULATORY MECHANISM; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETICS; HEK293 CELL LINE; HELA CELL LINE;

3' UNTRANSLATED REGIONS; ALZHEIMER DISEASE; BINDING SITES; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; HEK293 CELLS; HELA CELLS; HUMANS; MICRORNAS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 85007574972     PISSN: None     EISSN: 17589193     Source Type: Journal    
DOI: 10.1186/s13195-016-0186-x     Document Type: Article

References (54)

1. Gatz M, Reynolds CA, Fratiglioni L, Johansson B, Mortimer JA, Berg S, et al. Role of genes and environments for explaining Alzheimer disease. Arch Gen Psychiatry. 2006;63:168-74.
2. Harold D, Abraham R, Hollingworth P, Sims R, Gerrish A, Hamshere ML, et al. Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nat Genet. 2009;41:1088-93.
3. Hollingworth P, Harold D, Sims R, Gerrish A, Lambert JC, Carrasquillo MM, et al. Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat Genet. 2011;43:429-35.
4. Lambert JC, Heath S, Even G, Campion D, Sleegers K, Hiltunen M, et al. Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease. Nat Genet. 2009;41:1094-9.
5. Lambert JC, Grenier-Boley B, Harold D, Zelenika D, Chouraki V, Kamatani Y, et al. Genome-wide haplotype association study identifies the FRMD4A gene as a risk locus for Alzheimer's disease. Mol Psychiatry. 2013;18:461-70.
6. Naj AC, Jun G, Beecham GW, Wang LS, Vardarajan BN, Buros J, et al. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet. 2011;43:436-41.
7. Seshadri S, Fitzpatrick AL, Ikram MA, DeStefano AL, Gudnason V, Boada M, et al. Genome-wide analysis of genetic loci associated with Alzheimer disease. JAMA. 2010;303:1832-40.
8. Lambert JC, Ibrahim-Verbaas CA, Harold D, Naj AC, Sims R, Bellenguez C, et al. Meta-analysis of 74, 046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat Genet. 2013;45:1452-8.
9. Van Cauwenberghe C, Van Broeckhoven C, Sleegers K. The genetic landscape of Alzheimer disease: clinical implications and perspectives. Genet Med.doi: 10.1038/gim.2015.117.
10. Wei Z, Biswas N, Wang L, Courel M, Zhang K, Soler-Jover A, et al. A common genetic variant in the 3'-UTR of vacuolar H+-ATPase ATP6V0A1 creates a micro-RNA motif to alter chromogranin A processing and hypertension risk. Circ Cardiovasc Genet. 2011;4:381-9.
11. Papagregoriou G, Erguler K, Dweep H, Voskarides K, Koupepidou P, Athanasiou Y, et al. A miR-1207-5p binding site polymorphism abolishes regulation of HBEGF and is associated with disease severity in CFHR5 nephropathy. PLoS One. 2012;7:e31021.
12. Bao BY, Pao JB, Huang CN, Pu YS, Chang TY, Lan YH, et al. Polymorphisms inside microRNAs and microRNA target sites predict clinical outcomes in prostate cancer patients receiving androgen-deprivation therapy. Clin Cancer Res. 2011;17:928-36.
13. Nicoloso MS, Sun H, Spizzo R, Kim H, Wickramasinghe P, Shimizu M, et al. Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility. Cancer Res. 2010;70:2789-98.
14. Abelson JF, Kwan KY, O'Roak BJ, Baek DY, Stillman AA, Morgan TM, et al. Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science. 2005;310:317-20.
15. Gong Y, Wu CN, Xu J, Feng G, Xing QH, FuW, et al. Polymorphisms inmicroRNA target sites influence susceptibility to schizophrenia by altering the binding of miRNAs to their targets. Eur Neuropsychopharmacol. 2013;23:1182-9.
16. Delay C, Calon F, Mathews P, Hébert SS. Alzheimer-specific variants in the 3'UTR of amyloid precursor protein affect microRNA function. Mol Neurodegener. 2011;6:70.
17. Delay C, Dorval V, Fok A, Grenier-Boley B, Lambert JC, Hsiung GY, et al. MicroRNAs targeting Nicastrin regulate Aβ production and are affected by target site polymorphisms. Front Mol Neurosci. 2014;7:67.
18. Nicolas G, Wallon D, Goupil C, Richard AC, Pottier C, Dorval V, et al. Mutation in the 3' untranslated region of APP as a genetic determinant of cerebral amyloid angiopathy. Eur J Hum Genet. 2016;24:92-8.
19. Ambros V. The functions of animal microRNAs. Nature. 2004;431:350-5.
20. Sethupathy P, Collins FS. MicroRNA target site polymorphisms and human disease. Trends Genet. 2008;24:489-97.
21. Lewis BP, Shih I, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell. 2003;115:787-98.
22. Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol. 2005;3:e85.
23. Grimson A, Farh KKH, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007;27:91-105.
24. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136:215-33.
25. Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 2010;11:R90.
26. Sturm M, Hackenberg M, Langenberger D, Frishman D. TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics. 2010;11:292.
27. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003;5:R1.
28. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32(Database issue):D493-6.
29. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120:15-20.
30. Hu HY, He L, Fominykh K, Yan Z, Guo S, Zhang X, et al. Evolution of the human-specific microRNA miR-941. Nat Commun. 2012;3:1145.
31. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. An integrated map of genetic variation from 1, 092 human genomes. Nature. 2012;491:56-65.
32. Cogswell JP, Ward J, Taylor IA, Waters M, Shi Y, Cannon B, et al. Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways. J Alzheimers Dis. 2008;14:27-41.
33. Hébert SS, Horré K, Nicolaï L, Papadopoulou AS, Mandemakers W, Silahtaroglu AN, et al. Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer's disease correlates with increased BACE1/β-secretase expression. Proc Natl Acad Sci U S A. 2008;105:6415-20.
34. Denk J, Boelmans K, Siegismund C, Lassner D, Arlt S, Jahn H. MicroRNA profiling of CSF reveals potential biomarkers to detect Alzheimer's disease. PLoS One. 2015;10:e0126423.
35. Hébert SS, Wang WX, Zhu Q, Nelson PT. A study of small RNAs from cerebral neocortex of pathology-verified Alzheimer's disease, dementia with Lewy bodies, hippocampal sclerosis, frontotemporal lobar dementia, and non-demented human controls. J Alzheimers Dis. 2013;35:335-48.
36. Hébert SS, Horré K, Nicolaï L, Bergmans B, Papadopoulou AS, Delacourte A, et al. MicroRNA regulation of Alzheimer's amyloid precursor protein expression. Neurobiol Dis. 2009;33:422-8.
37. Leidinger P, Backes C, Deutscher S, Schmitt K, Mueller SC, Frese K, et al. A blood based 12-miRNA signature of Alzheimer disease patients. Genome Biol. 2013;14:R78.
38. Lau P, Bossers K, Janky R, Salta E, Frigerio CS, Barbash S, et al. Alteration of the microRNA network during the progression of Alzheimer's disease. EMBO Mol Med. 2013;5:1613-34.
39. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 2009;37(Database issue):D105-10.
40. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 2011;39(Database issue):D163-9.
41. Jansen BJH, Sama IE, Eleveld-Trancikova D, van Hout-Kuijer MA, Jansen JH, Huynen MA, et al. MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters. BMC Genomics. 2011;12:330.
42. Xiao Y, Xu C, Guan J, Ping Y, Fan H, Li Y, et al. Discovering dysfunction of multiple microRNAs cooperation in disease by a conserved microRNA co-expression network. PLoS One. 2012;7:e32201.
43. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004;2:e363.
44. Nam JW, Rissland OS, Koppstein D, Abreu-Goodger C, Jan CH, Agarwal V, et al. Global analyses of the effect of different cellular contexts on microRNA targeting. Mol Cell. 2014;53:1031-43.
45. Shulman JM, Imboywa S, Giagtzoglou N, Powers MP, Hu Y, Devenport D, et al. Functional screening in Drosophila identifies Alzheimer's disease susceptibility genes and implicates Tau-mediated mechanisms. Hum Mol Genet. 2014;23:870-7.
46. Sheffield LG, Miskiewicz HB, Tannenbaum LB, Mirra SS. Nuclear pore complex proteins in Alzheimer disease. J Neuropathol Exp Neurol. 2006;65:45-54.
47. Patel VP, Chu CT. Nuclear transport, oxidative stress, and neurodegeneration. Int J Clin Exp Pathol. 2011;4:215-29.
48. Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, Zhou XJ. Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation. PLoS One 2010;5:e8898.
49. Geekiyanage H, Jicha GA, Nelson PT, Chan C. Blood serum miRNA: noninvasive biomarkers for Alzheimer's disease. Exp Neurol. 2012;235:491-6.
50. Kiko T, Nakagawa K, Tsuduki T, Furukawa K, Arai H, Miyazawa T. MicroRNAs in plasma and cerebrospinal fluid as potential markers for Alzheimer's disease. J Alzheimers Dis. 2014;39:253-9.
51. Tan L, Yu JT, Hu N, Tan L. Non-coding RNAs in Alzheimer's disease. Mol Neurobiol. 2013;47:382-93.
52. Villa C, Ridolfi E, Fenoglio C, Ghezzi L, Vimercati R, Clerici F, et al. Expression of the transcription factor Sp1 and its regulatory hsa-miR 29b in peripheral blood mononuclear cells from patients with Alzheimer's disease. J Alzheimers Dis. 2013;35:487-94.
53. Wang WX, Rajeev BW, Stromberg AJ, Ren N, Tang G, Huang Q, al. The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. J Neurosci. 2008;28:1213-23.
54. Müller M, Kuiperij HB, Claassen JA, Küsters B, Verbeek MM. MicroRNAs in Alzheimer's disease: differential expression in hippocampus and cell-free cerebrospinal fluid. Neurobiol Aging. 2014;35:152-8.